The origin of the eukaryotic cell represents an enigmatic evolutionary puzzle. Ever since the discovery of the archaeal domain of life by Carl Woese and co-workers, Archaea have featured prominently in hypotheses for the origin of eukaryotes. According to Woese’s ‘universal tree’, eukaryotes and Archaea represent sister lineages, suggesting that Archaea and Eukarya emerged from a common ancestor. Whereas this classical ‘Three domains’ scenario has received considerable support in the past decades, recent studies have provided a growing support for cellular fusion scenarios in which eukaryotes emerged from within the archaeal domain of life. More specifically, the latest advanced phylogenomic analyses have indicated that eukaryotes form a monophyletic clade with the Lokiarchaeota, a group of archaea that was recently discovered in deep marine hydrothermal sediments. Analysis of the first reconstructed Lokiarchaeota genome revealed that it encoded numerous ‘eukaryotic signature proteins’ (ESPs), several of which are indicative of sophisticated membrane remodeling capabilities (actin, ESCRT proteins, small GTPases).
In our ongoing effort to gain insight in the archaeal origin of eukaryotes, we have now obtained metagenome data from numerous sites worldwide in order to obtain genomic data of uncultivated archaea. We have reconstructed the genomes of several novel archaeal lineages that are related to the Lokiarchaeota, some of which only distantly. Phylogenomic analyses indicate that these new archaeal lineages are united in a putative new superphylum that also includes eukaryotes. Detailed analysis of these new archaeal genomes revealed, in addition to ESPs previously identified in Lokiarchaeota, the presence of many new eukaryotic features. Altogether, the newly acquired data provide new, important insights in the enigmatic origin of eukaryotes.